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Agriculture Resource Guide Innovation Agriculture resource guide Innovation. Applied. Thermo Fisher Scientific is committed to providing instruments, reagents, and solutions for plant and animal research applications that will lead the way to remarkable agricultural discoveries—everything from improved crops to livestock that feed more people. We offer simple, scalable, and affordable solutions to help bring the next generation of agricultural products to life. 2 Thermo Fisher Scientific | Agricultural resource guide Contents Overview of agricultural applications 4 Plant and animal de novo genome sequencing 5 Plant and animal genotyping 7 QTL mapping and marker-assisted selection 12 Plant and animal gene expression analysis 15 Synthetic biology and genetic engineering 16 Plant cell and tissue analysis 18 GMO testing and detection 20 Sample preparation and nucleic acid isolation 22 thermofisher.com/agbio 3 Overview of agricultural applications This application resource guide will help you select our best products for some of the most common agricultural science applications. QuantStudio Genetic family of Ion Torrent TaqMan analyzers real-time PCR sequencers Assays systems QuantStudio QTL mapping & family of marker-assisted Ion Torrent real-time PCR selection sequencers systems Plant and animal TaqMan Genetic GMO testing de novo genome Assays and detection analyzers Objectives sequencing Higher yields Pest and environmental stress tolerance Healthier diets SimpliAmp GeneArt Thermal Cycler Precision TALs More efficient fertilizer use Higher quality meat Higher accuracy breeding values Phire QuantStudio Synthetic biology Higher feed conversion Plant and animal QuantStudio Direct PCR family of and genetic kits and real-time PCR genotyping Genetic family of master mixes systems engineering analyzers real-time PCR systems Invitrogen GeneArt Gene custom DNA Plant and animal Synthesis Ion Torrent TaqMan oligos gene expression sequencers Assays analysis GeneArt DNA Competent Ion assembly kits cells AmpliSeq for GBS Ion Torrent TaqMan sequencers Assays PCR Gateway enzymes cloning Qubit Fluorometer E-Gel with NanoDrop agarose gels Spectropho- tometer GeneArt CRISPR products and services 4 Thermo Fisher Scientific | Agricultural resource guide Plant and animal de novo genome sequencing Genome sequencing allows researchers to Ion S5 System uncover the genetic makeup of plants and animals. Sequencing plant and animal genomes is becoming easier and more cost-effective—this is true even for de novo sequencing projects aimed at obtaining the primary genetic sequence of your species of interest. We have an extensive portfolio of sequencing instruments, reagents, and analysis software to help get you there faster and with greater accuracy and reliability. Ion Chef System De novo sequencing solutions The Ion S5™ and Ion S5™ XL systems provide the simplest DNA-to-data workflow for targeted sequencing with industry- leading speed and affordability. So you can spend less time doing repetitive lab work and more time answering the critical questions in your research. These dramatic improvements in sequencing technology are changing the way agricultural scientists look at genomics and are paving the way for the next wave of remarkable agricultural discoveries. Ion Chef System templating made easy Genome sequencing for all The Ion Chef™ System makes next-generation sequencing Fast and affordable genome, exome, and transcriptome more accessible to agricultural scientists across the sequencing of plants and animals is accessible with the globe, offering: semiconductor sequencing technology in the Ion S5 systems. It empowers researchers to sequence his or • Automated template preparation and chip loading her economically important species, large or small. The • Cartridge-based reagent system system offers: • Sample- and reagent-tracking capability • Intuitive user interface • Chips with 60–80 million reads—ideal for exomes, • Application flexibility with 35–400 bp sequencing transcriptomes, and genotyping by sequencing • Onboard diagnostics • High accuracy • 2–4 hour sequencing run time Find out more at thermofisher.com/ionchef • Single-day sequencing of plant and animal genomes Find out more at thermofisher.com/ions5 Find out more and download case studies and technical information at thermofisher.com/plantdenovo thermofisher.com/agbio 5 6 Thermo Fisher Scientific | Agricultural resource guide Plant and animal genotyping The discovery of novel single-nucleotide polymorphisms (SNPs) is critical for plant and animal genotyping, as they serve as candidate markers for marker-assisted selection programs. Recent improvements in real-time PCR and next-generation sequencing have simplified SNP discovery and made it much more cost-effective. We offer a range of solutions to streamline all of your resequencing investigations and empower you to achieve your experimental and production goals. Why are SNPs important? Targeted resequencing and SNP analysis solutions SNPs are small variations in the DNA sequences that are Ion Torrent™ sequencers for targeted resequencing enable associated with desired traits. They are used in conjunction you to discover new SNPs in important crop genomes. with quantitative trait locus (QTL) mapping to develop assays Confirm your discoveries either with Applied Biosystems™ for marker-assisted selection programs aimed at improving TaqMan™ Assays or by Sanger sequencing on one of the or enhancing certain characteristics such as higher yield, Applied Biosystems™ genetic analyzers. better stress tolerance, or enhanced pest resistance. The table below compares the best genotyping solutions across our portfolio. Best experimental Research need Our platforms Why approach Compare sequences of Genotyping by Ion S5 and Ion Proton™ Speed, cost, scalability, simplicity several crop variants to sequencing (GBS) systems Ion Torrent™ systems enable fast discover functional SNPs and affordable GBS applications Map up to 10 SNPs in Fragment analysis SNP genotyping using Multiplexing capability: up to 10 different regions of the capillary electrophoresis (CE) SNPs per reaction genome genetic analyzers Map SNPs in a small region Sanger sequencing Sanger sequencing using CE Gold-standard technology for of the genome genetic analyzers sequencing Accuracy, low cost Simple workflow Confirm putative SNPs and Genotyping by Applied Biosystems™ Easy and fast workflow develop SNP assays for real-time PCR or TaqMan™ Sample-to-SNP™ High call rate and accuracy downstream work Ion AmpliSeq™ Kit Different formats for different technology Custom Applied project sizes (number of SNPs Biosystems™ TaqMan™ SNP combined with number of samples) Genotyping Assays and master mixes Real-time PCR instruments Ion Torrent™ sequencers Ion AmpliSeq™ consumables Find out more at thermofisher.com/gbs thermofisher.com/agbio 7 Plant and animal genotyping by sequencing Scalability, simplicity, and speed Genotyping by sequencing Two strategies for genotyping by sequencing Whether it’s used for the discovery and identification of The Ion S5 and Ion S5 XL next-generation sequencing SNPs or as a screen for panels of thousands of known systems support two different GBS strategies: markers, GBS using NGS technologies is a cost-effective • Ion AmpliSeq™ products for GBS: In cases where a set and unique tool for association studies and genomics- of SNPs has been defined for a section of the genome, assisted breeding in a range of plant and animal species— this approach uses PCR primers designed to amplify the including those with complex genomes that lack a reference targets of interest. View our complete solution for multiplex sequence. Ion Torrent sequencers are useful tools for GBS PCR below. Creating and ordering custom panels is easy due to their scalability, simplicity, and speed. with the Ion AmpliSeq™ Designer—a free, online assay design tool that enables custom design for any genome. Advantages of genotyping by sequencing with Ion S5 Use the preloaded bovine, chicken, pig, sheep, maize, and Ion S5 XL next-generation sequencing systems: tomato, soybean, and rice genomes to design your • Allow both SNP marker confirmation and de novo custom panel, or easily upload a FASTA file with your SNP marker discovery, even in cases where there is desired reference sequences for your genome no reference genome of interest. • Provide attractive, low-cost options for large numbers • Restriction enzyme (RE) digestion: The complexity of of samples and data points the genome is reduced by digesting the DNA with one • Utilize highly multiplexed sequencing to scale or two selected restriction enzymes prior to the ligation from thousands to millions of data points per day of sequencing adapters. Compared to the multiplex PCR • Enable 2–4 hour sequencing run times to approach, which is used for targeting known variants, this facilitate efficient planning for the next reproduction cycle method is better suited for situations where little genome sequence is available or no prior SNP variants have been • Offer a high degree of accuracy of SNP calling identified, for discovering new markers for marker-assisted • Offer versatility for many applications, including selection programs. de novo sequencing, targeted resequencing, and transcriptome sequencing Day 1 Day 2 1 DNA preparation 2 RE digestion/ 3 Ligate barcoded 4 Amplify library 5 Prepare template 6 Sequence 7 Analyze data multiplex PCR adapters fragments A. SNP verification: A. Ligation of amplification of targeted sequencing adapters For the multiplex PCR regions with custom (specific to
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